Contact Megan (mjpalmer@stanford.edu) if you have questions or need help using the wiki editing tools.

Contact Megan (mjpalmer@stanford.edu) if you have questions or need help using the wiki editing tools.

+

!!!Note we have now transitioned to editing via google doc: [https://docs.google.com/document/d/1quYEiPzyrLRs0txvox7DDu8wOJqWr1yGBRIIQ0uARNk/edit?hl=en_US here]

==Contributors==

==Contributors==

Line 36:

Line 37:

(tentative)

(tentative)

*Nov 26th: Last Day to Add Content to Wiki

*Nov 26th: Last Day to Add Content to Wiki

−

*Nov 27th: Meeting to Revise Letter

+

*Nov 27th: Meeting to Craft Letter

−

*Nov 29th: Letter Draft Circulation for Comments and Edits

+

*Dec 1st: Letter Draft Circulation for Comments and Edits

−

*Dec 2nd: Edits Due

+

*Dec 3rd: Edits Due

*Dec 4th: Final Letter editing

*Dec 4th: Final Letter editing

*Dec 6th: Responses Due

*Dec 6th: Responses Due

Line 89:

Line 90:

One grand challenge is the conversion of agricultural waste to useful products, such as fuels and pharmaceuticals. Engineered microbes like the yeast strain that produces artemisinic acid (Ro DK, Paradise EM, Ouellet M, et al. (April 2006). "Production of the antimalarial drug precursor artemisinic acid in engineered yeast". Nature 440 (7086): 940–3.) are a promising new technology, but they usually must be grown in precisely controlled environments and fed purified sugars in order to cost-effectively produce their product. The challenge, then, is to engineer microbes to accept a variety of compounds in agricultural waste as their carbon source. To encourage the development of such microbes, the Federal government should offer grants to academic and industrial researchers to engineer and optimize biosynthetic pathways that convert various organic products into simple sugars. - JVV

One grand challenge is the conversion of agricultural waste to useful products, such as fuels and pharmaceuticals. Engineered microbes like the yeast strain that produces artemisinic acid (Ro DK, Paradise EM, Ouellet M, et al. (April 2006). "Production of the antimalarial drug precursor artemisinic acid in engineered yeast". Nature 440 (7086): 940–3.) are a promising new technology, but they usually must be grown in precisely controlled environments and fed purified sugars in order to cost-effectively produce their product. The challenge, then, is to engineer microbes to accept a variety of compounds in agricultural waste as their carbon source. To encourage the development of such microbes, the Federal government should offer grants to academic and industrial researchers to engineer and optimize biosynthetic pathways that convert various organic products into simple sugars. - JVV

−

Improving DNA synthesis in terms of its quality, cost, and speed (i.e., 10kb scale, penny or nickel per base, and two week turnaround).

+

''-Aren't some of the national labs already working on this / funding academic labs to research it? - AC''

Improving DNA synthesis in terms of its quality, cost, and speed (i.e., 10kb scale, penny or nickel per base, and two week turnaround). Introduce some form of government or industry standard for acceptable DNA sequencing / synthesis quality. - AC

===Research & Development===

===Research & Development===

Line 101:

Line 105:

Synthetic Biology research center modeled after Bell Labs. ~ JW

Synthetic Biology research center modeled after Bell Labs. ~ JW

−

''-Would this be federally funded? Bell Labs was an industry research center. Would a federally funded single-site center be a better model than a SynBERC-type multi-institution academic-partner model? - AC''

+

''-Would this be federally funded? Bell Labs / Xerox PARC / Kodak / GE / IBM / DuPont had major corporate research centers. Would a federally funded single-site center be a better model than a SynBERC or JBEI-type multi-institution academic-partner model? Would it operate like the NIH campus or one of the national labs? - AC''

====Question 3====

====Question 3====

Line 109:

Line 113:

"Penny-per-base" DNA synthesis. See above. - AC

"Penny-per-base" DNA synthesis. See above. - AC

+

+

Sequencing genomes for organisms from which important natural products have been identified (e.g., approved pharmaceuticals or compounds that have been identified as having pharmacological activity). The DOE Joint Genome Institute may already be doing this. - AC

====Question 4====

====Question 4====

Line 119:

Line 125:

====Question 5====

====Question 5====

'''What are the barriers preventing biological research discoveries from moving from the lab to commercial markets? What specific steps can Federal agencies take to address these shortcomings? Please specify whether these changes apply to academic labs, government labs, or both.'''

'''What are the barriers preventing biological research discoveries from moving from the lab to commercial markets? What specific steps can Federal agencies take to address these shortcomings? Please specify whether these changes apply to academic labs, government labs, or both.'''

+

+

One of the reasons I've heard for the Bill and Melinda Gates Foundation to fund Amyris was the hope that once the central metabolic pathway / engineering tools / processing capabilities were developed and scaled up, similar metabolic engineering goals would cost far less money and time to develop and commercialize. Has this been the case? Has the government funded any metabolic engineering project on a similar scale, or could it try to develop strains of E. coli or S. cerevisiae that overproduce certain central or secondary metabolites for other labs to use? - AC

====Question 6====

====Question 6====

Line 125:

Line 133:

====Question 7====

====Question 7====

'''What high-value data might the government release in the spirit of its open government agenda that could spur the development of new products and services in the bioeconomy?'''

'''What high-value data might the government release in the spirit of its open government agenda that could spur the development of new products and services in the bioeconomy?'''

+

+

Organism genome sequencing data (DOE Joint Genome Institute may already be trying to do this). For metabolic engineering applications (e.g., biofuels or natural product pharmaceutical production), one major limiting factor is sequence information for enzymes that have not yet been characterized, which could potentially be identified through bioinformatic methods. Without access to sequence information, putative genes cannot be tested for enzyme activity. - AC

====Question 8====

====Question 8====

Line 137:

Line 147:

Greater emphasis on professional (rather than technical) development as part of a PhD. This could include opportunities external to lab like a practices workshop or internships in other sectors, but could also include more diverse activities as part of the research experience. Any efforts that encourage broader thinking and communication about synthetic biology, its broad goals and long term technological development would greatly benefit students who leave academia as well as those that continue to pursue academic careers. In the process, it may make sense to define more concretely the benefits and requirements of a PhD so that students interested in other facets of the discipline can explore other options. If a PhD is not necessary towards accomplishing social goals, we need other options such as MA programs that provide the necessary tools in a condensed timeframe. Engineers seems to be largely satisfied with a MA, perhaps there are parallels to that system ~ JW

Greater emphasis on professional (rather than technical) development as part of a PhD. This could include opportunities external to lab like a practices workshop or internships in other sectors, but could also include more diverse activities as part of the research experience. Any efforts that encourage broader thinking and communication about synthetic biology, its broad goals and long term technological development would greatly benefit students who leave academia as well as those that continue to pursue academic careers. In the process, it may make sense to define more concretely the benefits and requirements of a PhD so that students interested in other facets of the discipline can explore other options. If a PhD is not necessary towards accomplishing social goals, we need other options such as MA programs that provide the necessary tools in a condensed timeframe. Engineers seems to be largely satisfied with a MA, perhaps there are parallels to that system ~ JW

OSTP Request for Information on National Bioeconomy Blueprint

Background on the RFI

On September 16th, President Obama announced that his administration will develop a National Bioeconomy Blueprint detailing administration-wide steps to harness biological research innovations to address national challenges in health, food, energy, and the environment. By better leveraging America’s national investments in biological research and development, the Administration aims to stimulate the growth of high-wage, high-skill jobs while improving the lives of all Americans.

The White House Office of Science and Technology Policy (OSTP) has issued a Request for Information to solicit input from all interested parties on how best to develop the National Bioeconomy Blueprint. Comments can be submitted electronically as an email attachment to bioeconomy@ostp.gov by 11:59pm on December 6th, 2011.

SynBERC has encouraged every member of the synthetic biology community to submit their ideas to OSTP individually or in small groups. This is a unique opportunity to have your voice heard directly at the national level on issues that are of great importance to our community.

Wiki Purpose: Resources & Space for Collaborative Input

Members of the Practices Working Group have expressed interest in both submitting individual responses, and crafting a larger collective response. In order to help develop and refine our responses, we have created below spaces for collaborative developing and refining ideas and collecting relevant resources.

The seventeen specific requests for input outlined in the RFI are listed below.

Please add specific responses (most useful when in the form of complete but succinct ideas that we can pull together), comments and/or responses/feedback to others' ideas. Make sure attribute your contribution and list your name in the contributors section. Please include references where possible.

General references/resources should be added to the resources section.

Contact Megan (mjpalmer@stanford.edu) if you have questions or need help using the wiki editing tools.

RFI Detailed Information

General Info

OFFICE OF SCIENCE AND TECHNOLOGY POLICY (OSTP)

Request for Information: Building A 21st Century Bioeconomy

ACTION: Notice of Request for Information (RFI).

SUMMARY: The purpose of this Request for Information (RFI) is to solicit input from all interested parties regarding recommendations for harnessing biological research innovations to meet national challenges in health, food, energy, and the environment while creating high-wage, high-skill jobs.

The public input provided through this Notice will inform the Office of Science and Technology Policy (OSTP) as it works with Federal agencies and other stakeholders to develop a National Bioeconomy Blueprint.

DATES: October 7, 2011--December 6, 2011.

ADDRESSES: submit responses to BIOECONOMY@OSTP.GOV.

Supplementary Information

Purpose

The purpose of this Request for Information (RFI) is to solicit input from all interested parties regarding recommendations for harnessing biological research innovations to meet national challenges in health, food, energy, and the environment while creating high-wage, high-skill jobs.

The public input provided through this Notice will inform the Office of Science and Technology Policy as it works with Federal agencies and other stakeholders to develop a National Bioeconomy Blueprint.

Background

On September 16, 2011, President Obama announced that his Administration will develop a National Bioeconomy Blueprint detailing Administration-wide steps to harness biological research innovations to address national challenges in health, food, energy, and the environment. Biological research underpins the foundation of a significant portion of our economy. By better leveraging our national investments in biological research and development, the Administration will grow the jobs of the future and improve the lives of all
Americans.

Twenty-first century advances in biological research and technologies are poised to return tremendous public benefits. For example, advances in human genome-informed personalized medicine and data analytics could be combined to improve human health in novel ways. In bio-based industry, biological design can create new opportunities
for biofuels, chemicals, materials, and energy-efficient manufacturing processes.

The National Bioeconomy Blueprint will identify strategies to meet grand challenges, promote commercialization and entrepreneurship, focus research and development investments in areas that will provide the foundation for the bioeconomy, expand workforce training to prepare the next generation of scientists and engineers for the bioeconomy jobs of the future, identify regulatory reforms that will reduce unnecessary burdens on innovators while protecting health and safety, and describe appropriate public-private partnerships to accelerate innovation in key areas.

RFI Questions

OSTP seeks comment on the questions listed below to inform the development of the National Bioeconomy Blueprint:

Grand Challenges

President Obama has identified grand challenges as an important element of his innovation strategy, such as smart anti-cancer therapeutics that kill cancer cells and leave their normal neighbors untouched; early detection of dozens of diseases from a saliva sample; personalized medicine that enables the prescription of the right dose of the right drug for the right person; a universal vaccine for influenza that will protect against all future strains; and regenerative medicine that can end the agonizing wait for an organ transplant.

Question 1

Identify one or more grand challenges for the bioeconomy in areas such as health, energy, the environment, and agriculture, and suggest concrete steps that would need to be taken by the Federal government, companies, nonprofit organizations, foundations, and other stakeholders to achieve this goal.

One grand challenge is the conversion of agricultural waste to useful products, such as fuels and pharmaceuticals. Engineered microbes like the yeast strain that produces artemisinic acid (Ro DK, Paradise EM, Ouellet M, et al. (April 2006). "Production of the antimalarial drug precursor artemisinic acid in engineered yeast". Nature 440 (7086): 940–3.) are a promising new technology, but they usually must be grown in precisely controlled environments and fed purified sugars in order to cost-effectively produce their product. The challenge, then, is to engineer microbes to accept a variety of compounds in agricultural waste as their carbon source. To encourage the development of such microbes, the Federal government should offer grants to academic and industrial researchers to engineer and optimize biosynthetic pathways that convert various organic products into simple sugars. - JVV

-Aren't some of the national labs already working on this / funding academic labs to research it? - AC

Improving DNA synthesis in terms of its quality, cost, and speed (i.e., 10kb scale, penny or nickel per base, and two week turnaround). Introduce some form of government or industry standard for acceptable DNA sequencing / synthesis quality. - AC

Research & Development

R&D investments, particularly in platform technologies, can support advances in health, energy, the environment, and agriculture, and accelerate the pace of discovery in fundamental life sciences research.

Question 2

Constrained Federal budgets require a focus on high-impact research and innovation opportunities. With this in mind, what should be the Federal funding priorities in research, technologies, and infrastructure to provide the foundation for the bioeconomy?

Synthetic Biology research center modeled after Bell Labs. ~ JW

-Would this be federally funded? Bell Labs / Xerox PARC / Kodak / GE / IBM / DuPont had major corporate research centers. Would a federally funded single-site center be a better model than a SynBERC or JBEI-type multi-institution academic-partner model? Would it operate like the NIH campus or one of the national labs? - AC

Question 3

What are the critical technical challenges that prevent high throughput approaches from accelerating bioeconomy-related research? What specific research priorities could address those challenges? Are there particular goals that the research community and industry could rally behind (e.g., NIH $1,000 genome initiative)?

Sequencing genomes for organisms from which important natural products have been identified (e.g., approved pharmaceuticals or compounds that have been identified as having pharmacological activity). The DOE Joint Genome Institute may already be doing this. - AC

Question 4

The speed of DNA sequencing has outstripped advances in the ability to extract information from genomes given the large number of genes of unknown function in genomes; as many as 70% of genes in a genome have poorly or unknown functions. All areas of scientific inquiry that utilize genome information could benefit from advances in this area. What new multidisciplinary funding efforts could revolutionize predictions of protein function for genes?

Moving Life Sciences Breakthroughs from Lab to Market

It is a challenge to commercialize advances in the life sciences because of the risk, expense, and need for many years of sustained investment. The Administration is interested in steps that it can take directly, but is also interested in encouraging experimentation with new private-sector-led models for funding commercialization of life sciences research.

Question 5

What are the barriers preventing biological research discoveries from moving from the lab to commercial markets? What specific steps can Federal agencies take to address these shortcomings? Please specify whether these changes apply to academic labs, government labs, or both.

One of the reasons I've heard for the Bill and Melinda Gates Foundation to fund Amyris was the hope that once the central metabolic pathway / engineering tools / processing capabilities were developed and scaled up, similar metabolic engineering goals would cost far less money and time to develop and commercialize. Has this been the case? Has the government funded any metabolic engineering project on a similar scale, or could it try to develop strains of E. coli or S. cerevisiae that overproduce certain central or secondary metabolites for other labs to use? - AC

Question 6

What specific changes to Federal Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) programs would help accelerate commercialization of federally-funded bioeconomy-related research?

Question 7

What high-value data might the government release in the spirit of its open government agenda that could spur the development of new products and services in the bioeconomy?

Organism genome sequencing data (DOE Joint Genome Institute may already be trying to do this). For metabolic engineering applications (e.g., biofuels or natural product pharmaceutical production), one major limiting factor is sequence information for enzymes that have not yet been characterized, which could potentially be identified through bioinformatic methods. Without access to sequence information, putative genes cannot be tested for enzyme activity. - AC

Question 8

What are the challenges associated with existing private-sector models (e.g. venture funding) for financing entrepreneurial bioeconomy firms and what specific steps can agencies take to address those challenges?

Workforce development

Investment in education and training is essential to creating a technically-skilled 21st century American bioeconomy workforce.

Question 9

The majority of doctorate recipients will accept jobs outside of academia. What modifications should be made to professional training programs to better prepare scientists and engineers for private-sector bioeconomy jobs?

Greater emphasis on professional (rather than technical) development as part of a PhD. This could include opportunities external to lab like a practices workshop or internships in other sectors, but could also include more diverse activities as part of the research experience. Any efforts that encourage broader thinking and communication about synthetic biology, its broad goals and long term technological development would greatly benefit students who leave academia as well as those that continue to pursue academic careers. In the process, it may make sense to define more concretely the benefits and requirements of a PhD so that students interested in other facets of the discipline can explore other options. If a PhD is not necessary towards accomplishing social goals, we need other options such as MA programs that provide the necessary tools in a condensed timeframe. Engineers seems to be largely satisfied with a MA, perhaps there are parallels to that system ~ JW

Question 10

What roles should community colleges play in training the bioeconomy workforce of the future?

Continuing with my engineering education as a model theme, what role do community colleges play in these disciplines? ~ JW

Question 11

What role should the private sector play in training future bioeconomy scientists and engineers?

Continuing with my engineering education as a model theme, what role does the private sector play in training in these disciplines? ~ JW

Question 12

What role might government, industry, and academia play in encouraging successful entrepreneurship by faculty, graduate students, and postdocs?

Continuing...ah, you get the point ~ JW

Reducing Regulatory Barriers to the Bioeconomy

As President Obama has stated, our regulatory system must identify and use the best, most innovative, and least burdensome tools for achieving regulatory ends and protect public health, welfare, safety, and our environment while promoting economic growth, innovation, competitiveness, and job creation.

Question 13

What specific regulations are unnecessarily slowing or preventing bioinnovation? Please cite evidence that the identified regulation(s) are a) slowing innovation, and b) could be reformed or streamlined while protecting public health, safety, and the environment.

Question 14

What specific steps can Federal agencies take to improve the predictability and transparency of the regulatory system? (Please specify the relevant agency.)

Question 15

What specific improvements in the regulatory processes for drugs, diagnostics, medical devices, and agricultural biotechnology should federal agencies implement? What challenges do new or emerging technologies pose to the existing regulatory structure and what can agencies do to address those challenges?

Question 16

What are the highest impact opportunities for public-private partnerships related to the bioeconomy? What shared goals would these partnerships pursue, which stakeholders might participate, and what mutually reinforcing commitments might they make to support the partnership?

Question 17

What are the highest impact opportunities for pre-competitive collaboration in the life sciences, and what role should the government play in developing them? What can be learned from existing models for precompetitive collaboration both inside and outside the life-sciences sector? What are the barriers to such collaborations and how might they be removed or overcome?